Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	2,769,648	(C)6→7	intergenic (+162/‑55)	yfjQ → / → yfjR	CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	2,769,642	1	.	C	100.0%	180.6 / NA	49	intergenic (+156/‑61)	yfjQ/yfjR	CP4‑57 prophage; protein YfjQ/CP4‑57 prophage; putative DNA‑binding transcriptional regulator
Reads supporting (aligned to +/- strand):  ref base . (0/0);  new base C (26/23);  total (26/23)

TTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGG  >  NC_000913/2769508‑2769776                                                                                                                                        |                                                                                                                                        ttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑c                                                                                                                                   <  1:240037/140‑1 (MQ=255) ttAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑c                                                                                                                                   >  1:499155/1‑140 (MQ=255)  tAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑cc                                                                                                                                  <  2:383150/140‑1 (MQ=255)  tAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑cc                                                                                                                                  <  1:447368/140‑1 (MQ=255)  tAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑cc                                                                                                                                  <  1:459099/140‑1 (MQ=255)         ggACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTa                                                                                                                            <  1:34652/140‑1 (MQ=255)           acacCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTaaa                                                                                                                          >  1:399906/1‑140 (MQ=255)           acacCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGGTTCTCCGTTGTCCATACCCTGTCCG‑CCCCACCCCTTTaaa                                                                                                                          >  2:591686/1‑140 (MQ=38)             accaccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGt                                                                                                                        >  1:590303/1‑140 (MQ=255)               caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTaa                                                                                                                      >  2:667465/1‑140 (MQ=255)               caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTaa                                                                                                                      >  2:472180/1‑140 (MQ=255)               caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTaa                                                                                                                      >  1:686789/1‑140 (MQ=255)               caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑ccctct                                                                                                                              <  2:94706/131‑5 (MQ=255)               caccTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑cccc‑ccctct                                                                                                                              >  1:94706/1‑127 (MQ=255)                   tGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATcac                                                                                                                  <  2:499155/140‑1 (MQ=255)                    gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATcaca                                                                                                                 >  2:252340/1‑140 (MQ=255)                    gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATcaca                                                                                                                 <  1:608411/140‑1 (MQ=255)                    gTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATcaca                                                                                                                 >  1:274998/1‑140 (MQ=255)                         cATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCAtt                                                                                                            >  1:901148/1‑140 (MQ=255)                         cATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCAtt                                                                                                            <  2:590303/140‑1 (MQ=255)                            cGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTtc                                                                                                         <  2:179162/140‑1 (MQ=255)                                aTGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTtcagtc                                                                                                     <  1:640922/140‑1 (MQ=255)                                aTGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTtcagtc                                                                                                     <  2:840718/140‑1 (MQ=255)                                    gCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGtt                                                                                                 <  2:399906/140‑1 (MQ=255)                                           tgCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTc                                                                                          <  1:785950/140‑1 (MQ=255)                                             ccTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCt                                                                                        >  2:868574/1‑140 (MQ=255)                                             ccTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCt                                                                                        >  1:111805/1‑140 (MQ=255)                                                 aaTCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGgag                                                                                    <  1:667465/140‑1 (MQ=255)                                                   tCCCCCGGTTATAGCTTTTAACCCCCGTTATATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGaa                                                                                  <  1:746482/140‑1 (MQ=255)                                                     ccccGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtc                                                                                <  2:686789/140‑1 (MQ=255)                                                        cGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctct                                                                             >  1:549933/1‑140 (MQ=255)                                                        cGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAAtctct                                                                             >  1:317131/1‑140 (MQ=255)                                                               aGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGaca                                                                      >  2:361320/1‑140 (MQ=255)                                                                gCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGacac                                                                     <  1:472180/140‑1 (MQ=255)                                                                           ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGac                                                                       <  1:672693/127‑1 (MQ=255)                                                                           ccGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGac                                                                       >  2:672693/1‑127 (MQ=255)                                                                                      ggCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCg                                               >  1:839999/1‑140 (MQ=255)                                                                                       gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCgg                                              >  2:255803/1‑140 (MQ=255)                                                                                       gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCgg                                              >  2:858174/1‑140 (MQ=255)                                                                                       gCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTAATGACACAGGCAGAACGCCGCCATGACCgg                                              >  2:564717/1‑140 (MQ=255)                                                                                        cTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCggc                                             >  2:330535/1‑140 (MQ=255)                                                                                               aGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgt                                      <  2:901148/140‑1 (MQ=255)                                                                                                       aaaaTAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTggctgtcaggctgt                              <  1:330535/140‑1 (MQ=255)                                                                                                          aTAGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCAc                           <  2:549933/140‑1 (MQ=255)                                                                                                            aGTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTg                         <  1:361320/140‑1 (MQ=255)                                                                                                             gTTTCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGa                        >  2:740657/1‑140 (MQ=255)                                                                                                              tttCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGAt                       <  1:740657/140‑1 (MQ=255)                                                                                                              tttCTGCGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGAt                       <  1:69500/140‑1 (MQ=255)                                                                                                                    cGTTGTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAg                 <  2:317131/140‑1 (MQ=255)                                                                                                                        gTCCATACCCTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGt             <  2:274998/140‑1 (MQ=255)                                                                                                                               cccTGTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTg      <  1:252340/140‑1 (MQ=255)                                                                                                                                   gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:676346/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:702368/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:900122/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:396209/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:131631/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  2:393496/1‑140 (MQ=255)                                                                                                                                   gTCCGCCCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCggg  >  1:595650/1‑140 (MQ=255)                                                                                                                                        |                                                                                                                                        TTAATATCGGACACCACCTGTCCGCATCGCTATGTGCTCGTGTGCCTCAATCCCCCGGTTATAGCTTTTAACCCCCGTTACATCTGGCTTTTGCAGAAATAAAAAATAGTTTCTGCGTTGTCCATACCCTGTCCG‑CCCC‑CCTCTTTAAAGTAATCACATCATTTTCAGTCAGTTAACTTTCCTGGAGAATCTCTCATGACACAGGCAGAACGCCGCCATGACCGGCTGGCTGTCAGGCTGTCACTGATAATCAGCCGTCTGGTTGCGGG  >  NC_000913/2769508‑2769776

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 33 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑